From b5e86631b875407c2dfbd2ca7e54d13c75bc980c Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Mon, 13 Nov 2023 13:16:03 -0500 Subject: [PATCH] STY: Apply pre-commit --- .circleci/nipype.cfg | 2 +- Makefile | 1 - README.rst | 4 ++-- docs/_static/alabaster.css | 2 +- docs/_static/basic.css | 2 +- docs/_static/documentation_options.js | 2 +- docs/_static/language_data.js | 4 +--- docs/_static/pygments.css | 2 +- docs/_templates/apidoc/module.rst_t | 1 - docs/_templates/apidoc/toc.rst_t | 1 - docs/api.rst | 2 +- docs/installation.rst | 12 ++++++------ docs/usage.rst | 1 - wrapper/LICENSE | 2 +- 14 files changed, 16 insertions(+), 22 deletions(-) diff --git a/.circleci/nipype.cfg b/.circleci/nipype.cfg index 10451477e5..ed07e98c3c 100644 --- a/.circleci/nipype.cfg +++ b/.circleci/nipype.cfg @@ -1,4 +1,4 @@ [execution] stop_on_first_crash = true poll_sleep_duration = 0.01 -hash_method = content \ No newline at end of file +hash_method = content diff --git a/Makefile b/Makefile index 501071c083..89e6439f24 100644 --- a/Makefile +++ b/Makefile @@ -15,4 +15,3 @@ docker: --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \ --build-arg VCS_REF=`git rev-parse --short HEAD` \ --build-arg VERSION=`python setup.py --version` . - diff --git a/README.rst b/README.rst index c2aac2eb0b..0d7f2f12f4 100644 --- a/README.rst +++ b/README.rst @@ -7,7 +7,7 @@ sMRIPrep: Structural MRI PREProcessing pipeline .. image:: https://circleci.com/gh/nipreps/smriprep/tree/master.svg?style=shield :target: https://circleci.com/gh/nipreps/smriprep/tree/master - + .. image:: https://codecov.io/gh/nipreps/smriprep/branch/master/graph/badge.svg :target: https://codecov.io/gh/nipreps/smriprep :alt: Coverage report @@ -15,7 +15,7 @@ sMRIPrep: Structural MRI PREProcessing pipeline .. image:: https://img.shields.io/pypi/v/smriprep.svg :target: https://pypi.python.org/pypi/smriprep/ :alt: Latest Version - + .. image:: https://img.shields.io/badge/doi-10.1038%2Fs41592--018--0235--4-blue.svg :target: https://doi.org/10.1038/s41592-018-0235-4 :alt: Published in Nature Methods diff --git a/docs/_static/alabaster.css b/docs/_static/alabaster.css index 0eddaeb07d..969ce31601 100644 --- a/docs/_static/alabaster.css +++ b/docs/_static/alabaster.css @@ -698,4 +698,4 @@ nav#breadcrumbs li+li:before { div.related { display: none; } -} \ No newline at end of file +} diff --git a/docs/_static/basic.css b/docs/_static/basic.css index 0807176ec0..b8dbd02b95 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -673,4 +673,4 @@ div.math:hover a.headerlink { #top-link { display: none; } -} \ No newline at end of file +} diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index d47d15f79f..3ed4a153d9 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -7,4 +7,4 @@ var DOCUMENTATION_OPTIONS = { HAS_SOURCE: true, SOURCELINK_SUFFIX: '.txt', NAVIGATION_WITH_KEYS: false, -}; \ No newline at end of file +}; diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js index 5266fb19ec..f891ac1928 100644 --- a/docs/_static/language_data.js +++ b/docs/_static/language_data.js @@ -13,7 +13,7 @@ var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; -/* Non-minified version JS is _stemmer.js if file is provided */ +/* Non-minified version JS is _stemmer.js if file is provided */ /** * Porter Stemmer */ @@ -293,5 +293,3 @@ function splitQuery(query) { } return result; } - - diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css index dd6621d884..19bf02a9e8 100644 --- a/docs/_static/pygments.css +++ b/docs/_static/pygments.css @@ -74,4 +74,4 @@ .highlight .vg { color: #000000 } /* Name.Variable.Global */ .highlight .vi { color: #000000 } /* Name.Variable.Instance */ .highlight .vm { color: #000000 } /* Name.Variable.Magic */ -.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */ \ No newline at end of file +.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */ diff --git a/docs/_templates/apidoc/module.rst_t b/docs/_templates/apidoc/module.rst_t index 2490278551..49cca84bb8 100644 --- a/docs/_templates/apidoc/module.rst_t +++ b/docs/_templates/apidoc/module.rst_t @@ -6,4 +6,3 @@ {%- for option in automodule_options %} :{{ option }}: {%- endfor %} - diff --git a/docs/_templates/apidoc/toc.rst_t b/docs/_templates/apidoc/toc.rst_t index f0877eeb2f..878540cefe 100644 --- a/docs/_templates/apidoc/toc.rst_t +++ b/docs/_templates/apidoc/toc.rst_t @@ -5,4 +5,3 @@ {% for docname in docnames %} {{ docname }} {%- endfor %} - diff --git a/docs/api.rst b/docs/api.rst index b0c8205218..db8c6c94d5 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -8,4 +8,4 @@ Information on specific functions, classes, and methods. api/smriprep.cli api/smriprep.interfaces api/smriprep.utils - api/smriprep.workflows \ No newline at end of file + api/smriprep.workflows diff --git a/docs/installation.rst b/docs/installation.rst index a4c6d204b1..13431762be 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -56,10 +56,10 @@ You can check your `Docker Engine`_ installation running their ``hello-world`` i $ docker run --rm hello-world If you have a functional installation, then you should obtain the following output. :: - + Hello from Docker! This message shows that your installation appears to be working correctly. - + To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 1. The Docker daemon pulled the "hello-world" image from the Docker Hub. @@ -68,20 +68,20 @@ If you have a functional installation, then you should obtain the following outp executable that produces the output you are currently reading. 1. The Docker daemon streamed that output to the Docker client, which sent it to your terminal. - + To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash - + Share images, automate workflows, and more with a free Docker ID: https://hub.docker.com/ - + For more examples and ideas, visit: https://docs.docker.com/get-started/ After checking your Docker Engine is capable of running Docker images, then go ahead and `check out our documentation `__ to run the *sMRIPrep* image. -The list of Docker images ready to use is found at the `Docker Hub`_, +The list of Docker images ready to use is found at the `Docker Hub`_, under the ``nipreps/smriprep`` identifier. The ``smriprep-docker`` wrapper diff --git a/docs/usage.rst b/docs/usage.rst index 462502c542..f191307152 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -94,4 +94,3 @@ would be equivalent to the latest example: :: -v /path/to_output/dir:/out nipreps/smriprep:1.0.0 \ /data /out participant ... - diff --git a/wrapper/LICENSE b/wrapper/LICENSE index c4140b1eb0..26d2ab656b 100644 --- a/wrapper/LICENSE +++ b/wrapper/LICENSE @@ -24,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.